Matthew Stephens, Ph.D.


Research Description

My general interests include Bayesian and computational statistics, particularly when applied to problems in population genetics.  Specific interests include:

  • Estimating haplotypes from population genotype data (for which I distribute a software package PHASE).
  • Developing statistical models for patterns of linkage disequilibrium across multiple loci, and using these patterns to identify recombination hotspots.
  • Spatial modelling of allele frequency variation.

Selected Publications

False Discovery Rates: A New Deal.
Matthew Stephens
(2016) bioRxiv preprint

Visualizing spatial population structure with estimated effective migration surfaces.
Petkova D, Novembre J, Stephens M
(2016 Jan) Nat Genet. 2016 Jan;48(1):94-100. doi: 10.1038/ng.3464. Epub 2015 Dec 7. 26642242 (Full Text)

A Simple Model-Based Approach to Inferring and Visualizing Cancer Mutation Signatures.
Shiraishi Y, Tremmel G, Miyano S, Stephens M
(2015 Dec) PLoS Genet. 2015 Dec 2;11(12):e1005657. doi: 10.1371/journal.pgen.1005657. eCollection 2015 Dec. 26630308 (Full Text)

Efficient multivariate linear mixed model algorithms for genome-wide association studies.  Zhou X, Stephens M Nat Methods 11(4):407-9.

A Unified framework for association analysis with multiple related phenotypes. M Stephens PLoS ONE 8(7): e65245

A statistical framework for joint eQTL analysis in multiple tissues. T Flutre, X Wen, J Pritchard and M Stephens PLoS Genetics 9(5): e1003486. software

Polygenic modeling with Bayesian sparse linear mixed models. X Zhou, P Carbonetto and M Stephens PLoS Genetics 9(2): e1003264. software

Statistical inference of transmission fidelity of DNA methylation patterns over somatic cell divisions in mammals. A Q Fu, D P Genereux, R Stoger, C D Laird, and M Stephens. Annals of Applied Statistics 4(2): 871-892, June 2010

A nested mixture model for protein identification using mass spectrometry. Q Li, M MacCoss, and M Stephens. Annals of Applied Statistics 4(2): 962-987, June 2010

Using linear predictors to impute allele frequencies from summary or pooled genotype data. X Wen and M Stephens Annals of Applied Statistics 4(3): 1158-1182, September 2010

Analysis of population structure: a unifying framework and novel methods based on sparse factor analysis. B E Engelhardt, and M Stephens PLoS Genetics 6(9): e1001117. Software

Understanding mechanisms underlying human gene expression variation with RNA sequencing. J K Pickrell, J C Marioni, A A Pai, J F Degner, B E Engelhardt, E Nkadori, J B Veyrieras, M Stephens, Y Gilad, and J K Pritchard Nature, 464(7289):768-72, Mar 2010

Genome-wide association of lipid-lowering response to statins in combined study populations M J Barber, L M Mangravite, C L Hyde, D I Chasman, J D Smith, C A McCarty, X Li, R A Wilke, M J Rieder, P T Williams, P M Ridker, A Chatterjee, J I Rotter, D A Nickerson, M Stephens, R M Krauss PLoS ONE, Mar 2010 Supplementary results data page

Bayesian statistical methods for genetic association studies. M Stephens and D J Balding Nat Rev Genet, 10(10):681-90, Oct 2009

Practical issues in imputation-based association mapping. Y Guan and M Stephens PLoS Genet, 4(12), Dec 2008

Genes mirror geography within Europe. J Novembre, T Johnson, K Bryc, Z Kutalik, A R Boyko, A Auton, A Indap, KS King, S Bergmann, M R Nelson, M Stephens, and C D Bustamante Nature, 456(7218):98-101, Nov 2008

High-resolution mapping of expression-QTLs yields insight into human gene regulation. J B Veyrieras, S Kudaravalli, S Y Kim, E T Dermitzakis, Y Gilad, M Stephens, and J K Pritchard PLoS Genet, 4(10), Oct 2008

Combating the illegal trade in African elephat ivory with DNA forensics. S K Wasser, W J Clark, O Drori, E S Kisamo, C Mailand, B Mutayoba, and M Stephens Conserv Biol, 22(4):1065-1071, Aug 2008

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. J C Marioni, C E Mason, S M Mane, M Stephens, and Y Gilad Genome Res, 18(9):1509-1517, Sep 2008

Linkage disequilibrium-based quality control for large-scale genetic studies. P Scheet and M Stephens PLoS Genet, 4(8), 2008

Polymorphisms of the HNF1A gene encoding hepatocyte nuclear factor-1 alpha are accosicated with c-reactive protein. A P Reiner, M J Barber, Y Guan, P M Ridkerm L A Lange, D I Chasman, J D Walston, G M Cooper, N S Jenny, M J Rieder, J P Durda, J D Smith, J Novembre, R P Tracy, J I Rotter, M Stephens, D A Nickerson, and R M Krauss Am J Hum Genet., 82(5):1193-1201, May 2008

Interpreting principal component analyses of spatial population genetic variation. J Novembre and M Stephens Nat Genet, 40(5):646-649, May 2008

Imputation-based analysis of association studies: candidate regions and quantitative traits. B Servin and M Stephens PLoS Genet, 3(7), Jul 2007

Using DNA to track the origin of the largest ivory seizure since the 1989 trade ban. S K Wasser, C Mailand, R Booth, B Mutayoba, E Kisamo, B Clark, and M Stephens Proc Natl Acad Sci U S A, 104(10):4228-4233, Mar 2007